[EMBOSS] dbiflat and entret...

[Ted Chiang]

Jerome,

Thanks for your help.  Things seems to work pretty good.

-Ted


=====================================
Ted Chiang, Analyst
Centre for Computational Biology 
Hospital for Sick Children, Toronto
416.813.7028
tchiang at bioinfo.sickkids.on.ca
=====================================


On Sat, 6 Mar 2004, [ISO-8859-1] Jérôme Laroche wrote:

> Hi Ted,
> 
> Try this:
> 
> 1. dbiflat -fields taxon
> choose the right format of your flatfile: entry format
> 
> 2. Add the following lines in your .embossrc file:
> 
> DB swtest [
>     type: N
>     method: emblcd
>     format: genbank <-specify the format
>     dir: path    <- the path of your database
>     indexdir: path   <-the path of your index files
>     fields: org		<-the field you have indexed
> ]
> 3. seqret swtest-org:homo
> 
> I run a couple of test and it works. But you should knwo that not all 
> words in the field  ORGANISM are indexed. Just those of taxonomic 
> significance.
> 
> So in a genbank flatfile containing the following organism field for 
> two entries, the keywords 'Rhizobium/Agrobacterium group'  and 'dsDNA 
> viruses, no RNA stage' use together or alone were not recognized even 
> if they are in the organism field.
> 
>    ORGANISM  Agrobacterium sp.
>              Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;
>              Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium.
>   or
> 
>    ORGANISM  Chlorella virus
>              Viruses; dsDNA viruses, no RNA stage; Phycodnaviridae; 
> Chlorovirus.
> 
> 
> 
> Good luck!
> 
> 
> Jérôme
> Centre de bioinformatique
> Pavillon Charles-Eugène-Marchand
> Bureau 4233d
> tél: 418-656-2131 poste 6184
> fax: 418-656-7176
> www.bioinfo.ulaval.ca
>